To identify the genes that determine brain connectivity, Richiardi et al. mapped microarray-based gene expression data from human brain samples onto functional brain networks that were computed using resting-state fMRI data. Functional brain networks were recapitulated by gene networks based on the correlated expression of 136 genes. These genes were enriched for ion channels, and their expression was associated with axonal connectivity in mice, indicating that functional connectivity is strongly associated with synaptic function.